If you have a 50yrd zero, you're shots will be low below that range. At 7-15yrds, you'll have a Point Of Impact (POI) about 1.5 or so inches below the Point of Aim (POA) if you aren't adjusting for it. What range did you zero the weapon for?
As for the failure.. I'd run another 200-500 rounds through it and see if you're still having the issue. I think you might have had just a fluke malfunction.
As for ditching the USGI mags.. bah.. they work more than fine, have for longer than some of us have been alive. While I am a huge fan and proponent of the PMAG, I still have more USGI mags than PMAGs. Matter of fact I have about 20 USGI mags that have been following me around since 1993. Aside from adding the MagPul anti-tilt followers (most new generation USGI mags have a form of AT Followers) and ranger plates (which is better than the 550 cord and 100mph tape I used before) they have been my primary use mags for that whole time.
Learning to use the Iron sights is a very good skill to have for any weapon that has them. Optics do and will fail. While these days we have a wide variety of sight options, that is one of the greatest evolutions of the AR platform IMHO.
The traditional sights of the AR platform are well proven, designed to be handled by a person with an 8th grade education and have been used in every major gun fight the US military has been in since the 60's.. proven concept, I'd say so.
I'm an optics junkie myself, but I always zero the iron sights first, then move to the optic. I'm always adding or changing the options for my BUIS configurations, but they are always on the rifle.
Guess all I'm saying here with regards to the iron sights on your new rifle is that you stand to gain a whole lot by learning to use them correctly and to their fullest extent.